Secret Life of a Special Agent
by jessieleigh528
Summary: continuation of Life is Good. should read that first to get references. What happens when something goes wrong for Tony what choices does he have to make? and what confrontations come out of those decisions? is his secret almost out? Slash and implied Mpreg. if you dont like that then dont read. Review. Last chapter up
1. Chapter 1

**Secret Life of a Special Agent**

**A/N: So this is my second NCIS/Bones crossover fanfic. This is the second to my Life is good story. It doesn't begin in the beginning it's just a continuation one. I am still working on a prequel for Life is good. I'm just having writers block for that one. Constructive criticism would be greatly appreciated. This story is AU and may not follow much from the story just so you know. But anyway on to the story, I hope you enjoy!**

_Disclaimer: I wish I did but sadly I do not own these amazing characters. But if I did I would have them come together in the show, have Tony and Booth together with kids and everything else my way._

Sitting behind a desk all day doing cold cases was not Tony's idea of fun. Not that he wanted anyone to die or anything, he just hated not having a case.

All he could think about was his husband at work and his three kids at day care. His kids had grown up so quickly it was crazy. Jason and Jasper were already in their not-so-terrible-twos. They were good kids and always behaved but you had to always keep an eye on them. They were so mischievous and got into everything. His youngest, a bright little boy, Travis Bradley had just turned one year old. Trav had just started going to day care when before he would stay with his Uncle Steve and Aunt Jenna, who were long time friends with Tony.

No one at NCIS, or the FBI for that matter, knew he had a husband or kids. It isn't like he didn't want people to know or was ashamed of them of them he just liked to have his private life. It wasn't that hard to keep people away from certain topic. Tony just talked about his heterosexual love life that was nonexistent but no one ever questioned it.

Everyone thought he was a womanizing frat boy and he never tried to convince them they were wrong. He believed it was safer for his family by keeping his work life and personal life separately.

The ringing of Tony's phone brought everyone out of their concentration on their work.

"Hello, Very Special Agent Anthony DiNozzo speaking. How may I help you?" he said as nicely as he could causing Ziva and McGee to roll their eyes and Gibbs to continue with his work.

The smile dropped off of Tony's face only to be replaced with a frown. "How?... No if he's busy don't bother him… Yea I'm sure… Okay see you soon."

Looking over at Gibbs Tony got up and was packing his things. He then grabbed his gun to put it in the holster and put his badge in his pocket. "Boss, I need to leave now."

"What do you need to leave for?" Gibbs practically growled.

"Family emergency," Tony said.

"I thought you didn't have any family?" Ziva said with conviction.

"Yea didn't you say you didn't have any?" McGee added.

"Yes teams do not keep secrets from each other," Ziva expressed.

"Right like you two don't keep secrets. Like you shared about Rivkin and McGee like you shared about your sister possibly being a murder suspect! Yea real team sharing there." Tony practically yelled and turned back to Gibbs, "Well can I go?"

"Who in your family do you have to see?" Gibbs asked.

Tony sighed, "Does it matter who? Shouldn't it only matter that it's a _family emergency_?"

"I think he is lying if he does not want to tell you who the "emergency" is about." Ziva said with the usual air of arrogance she always had when she thought she was right. McGee nodded in agreement.

"You know what, fine I'm leaving I don't care. I need to be somewhere right now and I don't have to put up with this unprofessional and harassing treatment." With that Tony stormed to the elevator and disappeared.

"What was wrong with him? Can he not take it?" Ziva asked even though she knew the answer but just didn't care.

Everything in the squad went back to normal. Gibbs didn't like how his team was treating Tony or how Tony had a secret. He couldn't get the family emergency out of his head. He would stop by Tony's later maybe he'll get to the bottom of it. No he will get to the bottom of it.


	2. Chapter 2

**Secret Life of a Special Agent**

**A/N: So this is my second NCIS/Bones crossover fanfic. This is the second to my Life is good story. It doesn't begin in the beginning it's just a continuation one. I am still working on a prequel for Life is good. I'm just having writers block for that one. Constructive criticism would be greatly appreciated. This story is AU and may not follow much from the story just so you know. But anyway on to the story, I hope you enjoy! So just remember Tony is 31 and Seeley is 32. Tony was 20 and Seeley was 21 when they got married.**

_Disclaimer: I wish I did but sadly I do not own these amazing characters. But if I did I would have them come together in the show, have Tony and Booth together with kids and everything else my way._

Arriving home Tony turned off the vehicle and rested his head on the steering wheel. He couldn't believe he blew up like that in the bullpen. Of course it was justifiable but still he shouldn't have. Looking in to the rear view mirror brought a smile to his face, there sleeping in the back were his three amazing boys.

He had had to stop at the day care to pick up a sick Travis. So instead of having to make two trips he just picked up Jason and Jasper too. Seeley couldn't be reached probably due to a case. He sometimes wishes Seeley didn't have to work so much and had time for him and the kids. He wasn't complaining though, he knew what the job was like.

Finally getting out of the truck Tony moved to the other side and opened the back door. Pulling out the double stroller from the back, Tony placed both sleeping two year olds, Jason and Jasper, into the seats and strapped them in. He then pulled Trav and carried him while pushing the stroller up to the house. He soon had the front door locked and moved to the twins' room. Gently placing both into their own cribs, Tony gave them both a kiss on their foreheads. He then moved to Travis' room to change and clothe him for bed. Soon he was asleep in his crib.

Moving to his bedroom he turned both baby monitors on and changed into sweats and a long sleeve t-shirt. Feeling drained and exhausted Tony curled into bed and was soon pulled into a restful and dreamless sleep.

The house was silent as he entered the front door. Work had ended fairly early so Seeley was able to leave that much sooner. He listened to his voicemails about Travis being sick and felt guilty because Tony was stuck doing everything by him self like usual.

Opening the twins' door Seeley peaked in to see they were still asleep. He smiled affectionately at his first born sons and gave them each kisses on their sandy brown locks on their little heads. He moved to Travis' room.

As he opened the door he saw Travis staring at him with Tony's intense eyes that seemed more mature than they were. His little cheeks were flushed with fever and he looked every bit as sick as he was.

"What Baby Boy, couldn't sleep?" Seeley whispered as he made his way to pick Travis up. Walking him around usually helped him go back to sleep. Just as he was leaving Travis' room he heard the doorbell.

"Huh, I wonder who that could be, huh Trav?" Seeley asked as he pulled Travis closer to him.

Opening the door Seeley recognized the man by the stories he was told, "Can I help you?"

Seeley saw the curious look pointed at him then Travis. But when Travis looked at Gibbs, Gibbs' brows furrowed.

"Who is the boy? Is he related to Tony?" Gibbs asked noticing the boy had the same eyes as Tony's.

"Well yea I would thing he was related to his son," Seeley said being slightly sarcastic but with a smile.

The look on Gibbs' face was priceless, he looked about to have a conniption. "Tony has a son?" his tone was one of incredulousness.

"Yes, he has three. This is just the youngest."

"Who is the other parent? And who are you?"

"Well first I am and I am their father and Tony's husband for eleven years."

"How come he never talks about you then?"

"It's safer that way. You know with jobs like ours it's not safe with people knowing you have a family when they can use that against you for revenge."

Gibbs just nodded.

Travis began to squirm and looked like he was going to start crying.

"Do you want to come in? I need to give Trav some medicine."

"Sure," Gibbs answered following Booth in.

"Sorry about before I was just curious as to why you were here. I'm Seeley Booth," he offered along with his hand extended out towards Gibbs.

"Jethro Gibbs, Tony's boss but you probably already knew that." Gibbs reciprocated the handshake.

Seeley turned around and opened the fridge. Grabbing out the medicine Booth measured out the amount and put it into a syringe. Gently he placed the syringe into Travis' mouth and pressed down the pump sending the medicine into his mouth.

Travis didn't look too happy with the taste and got red faced. He began to tear up and soon busted out crying.

"Oh come on Baby Boy. There is no need for that now. It's just medicine to make you feel better. Come on shhh. Booth continued to bop Travis gently up and down and say reassuring things into his silky brown wavy locks with kisses.

Gibbs' heart constricted just thinking about doing the same thing for Kelly as a baby.

The crying seemed to attract someone, hearing a door open Seeley looked up.

"Hey sorry to wake you up, Trav just needed his meds." Booth said lightly when he spotted his husband in sweats and his dark grey FBI long sleeve t-shirt.

Smiling lightly Tony shook his head, "its okay I just heard my Baby Boy crying," Tony said grabbing Travis from Seeley. When Travis got into Tony's arms he suddenly stopped crying and was soon asleep.

"I still have no idea how you do that," Booth said trying to look mad but failed when the corner of his mouth went up.

"I'm just amazing what can I say?" Tony asked laughing. Giving Booth a kiss Tony was about to deepen it when he heard some one clearing their throat.

Startled Tony turned around and held Travis closer to his body.

"Boss?!" Tony squeaked not at all anticipating the turn of events.

**TBC**


	3. Chapter 3

**Secret Life of a Special Agent**

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"_I'm just amazing what can I say?" Tony asked laughing. Giving Booth a kiss Tony was about to deepen it when he heard some one clearing their throat._

_Startled Tony turned around and held Travis closer to his body._

"_Boss?!" Tony squeaked not at all anticipating the turn of events._

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"Boss what are you doing here?" Tony was trying his best not to look nervous. He looked between Booth and Gibbs, looking for an explanation.

"I wanted to make sure that the emergency was okay and to say that that attitude in the bullpen towards you will not happen again."

Knowing that was the closest thing he would get of an apology Tony smiles, "Thanks Boss. Um yea the emergency is getting there. Travis here was sick and I was the only one who could go and get him."

"Well that's good. He's an adorable kid," Gibbs said with a smile as he looked at Travis who looked like a mini version of Tony. They had the same eyes and the same soft looking strands of chestnut brown hair. Gibbs could imagine they would have the same smile too if Travis wasn't sick. There was almost no part of Booth in the boy's features.

"Thanks," Tony and Booth both spoke at the same time bringing a smile to both of their faces. "Boss, would you like some coffee or something?"

"Sure, I could definitely go for some coffee."

Booth then excused himself from the room, to check on the twins, taking a sleeping Travis with him to put him in his room.

Gibbs observed Tony as he was working on the coffee; he didn't look or act any different. How could he have missed that Tony had a family: a husband to begin with and three kids. 'So much for being a good investigator' Gibbs thought grudgingly to himself.

"Nobody really knows about my other life Boss," Tony spoke up bringing Gibbs out of his thoughts. "Not even Seeley's colleagues know about us or the kids." Tony had turned around to look at Gibbs.

Gibbs could only nod. Looking around the house Gibbs felt the house had a lot of love in it and had a lived in feel to it. There were toys neatly pilled into a toy box in the corner, baby blankets folded on the side of the couch, 2 playpens towards the back wall and a few stuffed animals and toys in each. He had always believed that Tony could have the best of both worlds: the job he loved and a family. Only now he realized Tony already had both and seemed happy with it. He had always thought he had had a chance to give that life to Tony, but sitting here in Tony and another man's kitchen, observing things that belonged to their children, Gibbs knew not to try anything no matter how much he wanted to. Just wrap Tony up in his arms, kiss him senseless and beg him to run away with him and the kids. It was a long shot he knew that's why it was only a thought and not turned into an action.

"Boss, can you not tell anyone about this, we're trying to keep it quiet? You never know what someone would try to use against you and I really can't lose my kids, I just don't know what I would do."

"It's not a problem; this can just stay between you and me. I wouldn't ruin your trust by saying anything that is not anyone's business but yours. And I wouldn't want anything to happen to your kids because I couldn't keep my mouth shut."

"Thank you Gibbs." Tony gave him a grateful smile then turned around and poured the coffee into a cup that said FBI on it and handed it to Gibbs. Tony had to laugh at the face Gibbs made when he was handed the cup.

"Oh just drink it. I promise I won't tell anyone about it."

"Good you better not." Grinned Gibbs and added, "I have a reputation to uphold." Tony barked out a laugh at that.

The sound of pitter pattering feet made them both look up just in time to see two blurs to launch themselves at Tony, who scooped them up readily like they did this many times before. Tony then proceeded to blow raspberries on their tummies drawing high pitched but adorable giggles from them both bringing a smile to Tony and Gibbs' faces.

"Daddy! Daddy stop!" They both yelled breathlessly in unison from the continuous laughing.

Laughing Tony stopped his actions, "Okay, okay. So how were your naps?"

"Good Daddy, we sleeped really long!" Jason spoke up while Jasper continued to nod his head vigorously. They both held onto Tony tight and gave him sloppy kisses to his cheeks, which only made his smile bigger.

"Okay boys you can meet my boss, this is Gibbs. What do you say?"

"Hi Boss," Jason said while waving his little hand. "Nice to meet you," Jasper added with his own wave.

"Hi boys, what are your names?" Gibbs couldn't suppress his smile with Tony's two adorable twin sons.

"He's Jasper and I'm Jason." Jason proceeded to point them both out while talking. Jason was always the more forward of the two while Jasper was the more quiet one.

"Well hello Jason and Jasper." Gibbs then turned to Tony and added, "How old are they?"

"They're two years old and tuning closer to three everyday." Tony's whole face lit up when he talked about his precious children.

"I know how that goes. They grow up so quick it seems the time flies away." Gibbs' eyes got that far away look they usually got when he thought about Shannon and Kelly. He mentally shook himself to keep the topics light.

Tony gave him a sad but knowing smile and nodded, "Yea that is does." He then looked to his sons in his arms and gave them both kisses on their dark locks. "Why don't you guys quietly go play in the living room, okay?" As they were about to run away Tony added, "Play quietly! You know your brother needs his sleep."

"Yes Daddy!" Said the excited two year olds in unison.

Gibbs just laughed and shook his head. As he looked at Tony watching his boys play he deduced that fatherhood was a very good look on Tony. 'If I had only acted sooner this could be my life with Tony watching our children play,' kept going through his head 'yea right it would have had to be around eleven years before.'

Seeley then walked into the kitchen again and put an arm around Tony's waist and kissed his head before going over to the coffee machine. As he was making himself a cup he followed the others' gazes and it landed on his sons playing. It brought a knot to his stomach thinking about his happy family and what his mistake could do to it.

Soon Gibbs had to leave and was walked out by Tony, which is how he found himself now sitting in his car thinking about things. Thinking about all the mistakes he had made and all of the chances he missed because he was too stubborn. He vowed to himself if he got the chance to have everything he wanted he would not hesitate to take it.

Finally sighing Gibbs looked at the house one more time and drove to his empty and forlorn house and hoped that morning would come soon to end the lonely night.

TBC… Soon


	4. Chapter 4

**Secret Life of a Special Agent**

_Seeley then walked into the kitchen again and put an arm around Tony's waist and kissed his head before going over to the coffee machine. As he was making himself a cup he followed the others' gazes and it landed on his sons playing. It brought a knot to his stomach thinking about his happy family and what his mistake could do to it._

_Soon Gibbs had to leave and was walked out by Tony, which is how he found himself now sitting in his car thinking about things. Thinking about all the mistakes he had made and all of the chances he missed because he was too stubborn. He vowed to himself if he got the chance to have everything he wanted he would not hesitate to take it. _

_Finally sighing Gibbs looked at the house one more time and drove to his empty and forlorn house and hoped that morning would come soon to end the lonely night. _

Gibbs had just started working on the boat when he heard the knocking. No one had knocked on his front door that knew him because he always left it unlocked. But who would be at his house at this hour?

When he finally made it upstairs he was shocked as he pulled open the door. Standing there was Tony and his boys.

From observing Tony he could tell that he had been crying recently. His twins were both asleep in the double stroller while Travis was asleep in his arms. A diaper bag was slung over his left shoulder.

"Come in Tony, you didn't have to wait outside or knock. Here let me take the twins and your bag." Tony only nodded as he handed over the bag and stroller. Gibbs then ushered him inside the house into the seldom used living room.

"Why don't we put these guys down in the guest room? There's plenty of room." Once again he was only met with a silent nod.

Gibbs unstrapped the stroller's straps and grabbed each twin up into his arms. They both snuggled deeper into his arms and Jasper started sucking on his thumb which brought a smile to Gibbs' face.

When they reached the guestroom Gibbs laid the twins on the full sized bed and put pillows around them so they wouldn't fall on the ground by rolling around. Gibbs took the baby monitor, which Tony packed, out of the diaper bag and turned it on. He put the side lamp on as a night light and quietly left the room. He then walked over to a room Tony had never seen open and soon came back with a beautiful crib.

Tony startled at seeing the crib. "Gibbs you don't need to bring that out. I can have Travis sleep with me on the couch, its fine."

Gibbs only ignored him and walked over to the master bedroom and put the crib close to the bed. He then took a sleeping Travis from Tony and placed him in the crib gently and placed a blanket on his small form. Luckily there was two baby monitors packed so each room could have one. Switching the lamp on Gibbs left the room with Tony following close behind.

"So are you going to tell me what happened?" Gibbs asked softly.

"Um… Seeley and I… had a fight. And um I don't see it ever getting better. It's over between us for good. I didn't know where else to go so I came here. Being in the house was just too much for me." Tony had tears rolling down his cheeks as he remembered everything that happened.

"What was the fight about?" Gibbs was angry at the FBI agent for making Tony ever cry. Tony then began to tell Gibbs what happened.

****§Flashback§****

After he had put the kids to bed, Tony made his way upstairs to Seeley and his bedroom. As he entered the room he saw Seeley just standing there not really looking at anything in particular. It was odd for him to just stand around, he always seemed to be doing something and always being on the move.

Tony walked over and gave Seeley a hug. What shocked Tony was at first Booth stiffened and finally returned the hug. Looking up at Booth, Tony saw something in Booth's face that worried him.

"Hey what's wrong?" Tony asked not understanding what was wrong.

As Seeley looked down at Tony he finally found his voice, "We need to talk."

Tony's stomach went into a knot as he was led over to the bed where they both sat down and faced each other. Booth took his hand between his.

"Remember when that guy I worked with died and I had stayed at the apartment I keep, to keep up appearances for work? Well I… I wasn't alone. My colleague Temperance "Bones" was there too. And later she was crying so I told her to lay with me." By then Tony's stomach had dropped, making him feel sick. But Seeley kept going, "And it just happened and we slept together. But she told me that she's… um she's pregnant, with my baby." Tony pulled his hand away and just sat there. His throat began to feel full like it always did when he was close to tears.

"Say something, anything." Booth broke the silence.

"Get out, now. You can't stay here anymore." Tony spoke in a quiet but stern voice that spoke volumes about how he was feeling. Looking into Seeley's eyes Tony added, "I want a divorce and I'm taking the kids. Now get out of my house, now."

Seeley nodded and before he left he looked back and saw Tony in the same spot. He had never seen Tony like this before and he hated himself for being the one to do this to Tony. 'How could you be such an idiot Booth?'

The sound of the door being shut reverberated in Tony's head signaling the end to his eleven year love. He knew that everything was done between them. He would never put up what his mom had with his father even though it was never to the same extent.

Tony couldn't hold his emotions in any longer, he curled up in on himself and cried. He cried for the love that was lost, for the man he believed his husband was, for his kids who would be put in the middle of everything and for himself. He had to learn to live independently again and as a single parent.

He finally stopped crying. No he would stop feeling sorry for himself; he didn't need Booth to care for him or the boys. He had been doing everything for the boys and Booth had only been there occasionally.

Being in the house that had been theirs for longer than five years though was too much on him right now. Even though Seeley was not there at the moment there were memories all throughout the house at every turn. He feared if he didn't leave soon he would take Seeley back and end up as one of the people who always went back after all of the mistakes their others did.

He packed up the kids with everything they needed and put them in the truck. He drove to the only place he could think of, the only place he felt safe; Gibbs' house.

****§End Flashback§****

Gibbs was shocked he would have never guessed that that was what happened. He looked over to Tony and saw him crying so he pulled him into a tight hug.

That seemed to loosen something in Tony because a dam seemed to have been broken and all of Tony's emotions poured out.

Gibbs continued to run his fingers through the soft chestnut strands of hair that were softer than he thought. A little under ten minutes ago Tony's breath had evened out signaling he had finally gotten to sleep.

Gibbs didn't want to wake Tony but sleeping like this would end in a very sore day tomorrow so Gibbs gently prodded Tony awake.

"Come on Tony you have to get up, you should move to the upstairs bedroom."

Tony's reply was to mumble and snuggle into Gibbs' chest more. Gibbs really liked the feeling of having a warm body in his arms again but the best part of it is that it was Tony; the man he had loved for years.

"Okay fine, but I'm only doing this once." Gibbs then grabbed Tony and picked up. He was lighter than Gibbs once believed.

When he mad it to the master bedroom Gibbs placed Tony down and pulled the covers up over him.

As he was walking away Tony seemed to have another idea. Gibbs found himself on top of the bed with Tony cuddled up next to him. Tony's hand had the front of his shirt in a death grip and his head on Gibbs' chest. Gibbs' knew he should stop this but he loved the feeling of Tony in his arms and having Tony's kids in the same house. He would protect Tony and Tony's boys with everything he had even from one Seeley Booth.

He was soon hypnotized by the sounds of four sets of even breathing that he was soon pulled into a restful sleep.

**TBC: Soon. I love reviews so please leave them ! Also I know where the story is going so it will be updated hopefully soon. Everything will be answered later for anyone who has questions about the story. **


	5. Chapter 5

**Secret Life of a Special Agent**

_As he was walking away Tony seemed to have another idea. Gibbs found himself on top of the bed with Tony cuddled up next to him. Tony's hand had the front of his shirt in a death grip and his head on Gibbs' chest. Gibbs' knew he should stop this but he loved the feeling of Tony in his arms and having Tony's kids in the same house. He would protect Tony and Tony's boys with everything he had even from one Seeley Booth._

_He was soon hypnotized by the sounds of four sets of even breathing that he was soon pulled into a restful sleep. _

Gibbs felt more rested then ever before as he woke up from the sun shining in his eyes. He looked down and realized why. Tony looked completely at rest and years younger in his sleep. Gibbs wanted nothing more than to be able to wake up just like this every morning and to sleep beside this man for the rest of his life.

Looking over Gibbs saw two little green eyes staring back at him. Travis must have woken up because he was rubbing his little eyes.

Gibbs extracted himself from Tony's grip, he then rolled over and hugged Gibbs' pillow close. Gibbs would have never used cute to describe a man but that was exactly the way to describe most of the things Tony did.

Gibbs' happy mood diminished when he heard the uttering of one word by Tony, "Seeley." But he then remembered he had company who needed his attention so he plastered a smile on his face that turned genuine when he saw little Travis. He could never stay upset when dealing with children especially one of Tony's.

"Hey little man, you want some breakfast? I bet you're hungry, huh?" Gibbs realized he missed having a baby in the house and being able to care for one.

Travis shook his head yes and lifted his arms up to be picked up.

Laughing quietly, Gibbs lifted Travis up and gave him a light kiss to the forehead. He checked in on the twins to see if they were hungry as well, only to see that they were still sleeping soundly.

"Okay now let's see what food there is to give you." Gibbs made faces at Travis as he looked at all the baby food jars that were packed in his diaper bag.

"So there is nothing here that looks appetizing is there? What has your daddy been feeding you?" Gibbs asked while looking at Travis who giggled. Gibbs began to look through the seldom used cabinets and found something that almost everyone liked to eat no matter what age; Cheerios.

Once Gibbs got him and Travis situated at the table Gibbs poured a bowl of the cereal and put them close to Travis. His little hands took one and investigated what it was. He hesitantly brought one to his lips after he saw Gibbs do the same. A smile formed on his tiny face as he brought more to his open mouth. His slobbery fingers continued to bring the delicious treat to his mouth.

"Oh, thank you," Gibbs replied as Travis forced a Cheerio into Gibbs' mouth. "Mmm, thank you Travis it was yummy, but now you eat them okay?"

Gibbs turned towards the door way seeing a smiling Tony observing the whole scene. As soon as Travis looked over, he jumped up on Gibbs' lap and started grabbing the air for Tony with sticky little hands.

Giving a chuckle, Tony walked over and obliged Travis' wish. Hugging his baby close Tony closed his eyes and drew in a long breath of Travis' baby scent. He found the special scent of his kids to be one of the only things that could relax him.

Travis began wiggling in Tony's arm until he looked down at Travis. "What baby boy?"

Travis didn't act like this very often. A smile soon graced Tony's face when he saw what Travis wanted; none other than Gibbs. "Well I think my son would rather be with you and your Cheerios." Tony chuckled as he handed Travis over bringing a smile to Gibbs' face.

"What can I say, the kids got good taste." Gibbs replied with a sheepish smile. Tony knew that was as close to an apology as he was going to get.

Tony shook his head, "No its okay. I'm just surprised, that's all, Travis just never lets anyone hold him while he's eating except for me and… well you know. But I'm glad he lets you."

"I'm glad too." Gibbs went back to helping Travis with his breakfast.

Tony began going through Gibbs' cabinets looking for something for the twins to eat. Just then the sound of pitter pattering of small feet could be heard coming from upstairs.

"No running!" Tony yelled and was soon graced with seeing the boys slowly walking into the kitchen. They both donned sheepish smiles as they tried to look like they weren't doing anything wrong and were the poster boys for innocence.

"Here have some cereal so I can get you ready for school." The twins like usual, ate like they had never eaten before they got that from both of their dads who could put away a lot of food but never grow an inch.

After the kids were dropped off at day care, Tony drove back to Gibbs' house.

Once inside the house Tony waled down to the basement and sat on "his" step. The sound of Gibbs sanding always soothed him and he was feeling more relaxed. Just as he was getting comfortable, Gibbs shattered it.

"So have you talked to Seeley?"

**TBC.**

**A/N: I know, I know I'm so late with this. Everything in my life is seemingly happening at the same time. My school work is overwhelming, my job keeps me busy and so does extracurricular activities that I keep missing because of my busy schedule. Then my grandmom got into a car accident and is in rehab and over Christmas too, but she alright so I'm thankful. I got the best present ever I got a truck! And I love it. I promise I will try to be better with my posting. I'm already working on the next chapter so I hope that's out soon. **

**So should this story stay Tony/Seeley or Tony/Gibbs. Review and let me know cause right now I'm not totally sure.**


	6. Chapter 6

**Secret Life of a Special Agent**

_After the kids were dropped off at day care, Tony drove back to Gibbs' house._

_Once inside the house Tony walked down to the basement and sat on "his" step. The sound of Gibbs sanding always soothed him and he was feeling more relaxed. Just as he was getting comfortable, Gibbs shattered it. _

"_So have you talked to Seeley?"_

Tony just shook his head. Everything was still so new; he didn't know how to react. How were you supposed to react to that kind of news anyway? Your husband of eleven years, the father of your children and your soul mate first cheats on you and then finds out he is the father to some other woman's unborn baby. It was something off of one of those stupid soap-operas.

"Well, maybe you should. Just listen to his side of the story and try to work it out. Think of your kids and their feelings. How will they be without their father? Everyone makes mistakes, are you willing to throw eleven years away over one?"

Tony just looked wide eyed. He wasn't sure if he could live with any more heart break. What if Seeley didn't love him anymore or didn't want to be with him anymore? Or what if he tries to take the kids away from him? he knows that's hypocritical to say when that's close to what he did to Seeley but he only has the kids Booth has that woman and their kid in the end. But how will the kids live with growing up in two different households if he and Seeley cannot over come their differences?

He couldn't get over the love though. Seeley and he had been together for too long to throw it away, he knew that but he still couldn't let go. He couldn't let go of the hurt, the betrayal by the man who promised and vowed to always love him till death do they part.

How would his life be if he took Seeley back? Would he have to deal with the other woman or would Seeley still be with her? Would he always leave early on holidays, birthdays or days in general to be with them? And if Seeley got away with cheating once by him taking Seeley back, would he think if he continues he'll always be able to come back?

The uncertainty scared Tony; he didn't do well with it. He needed order and guidelines; he wasn't as easy going as everyone thought he was.

One thing he was certain about is that if this hadn't of happened he would have grown old with Seeley, seen their children grow up and do everything together. They were each other's soul mate, still were.

He knew Gibbs was right; he needed to talk to Seeley about everything. It was the only way to get to the bottom of everything.

Thoughts of Seeley's work partner 'Bones' went into his head. He knew that she always had a thing for Booth, but he didn't think anything would come out of it. She was always trying to get him to do things with her. That's when another thing popped into his head. Would she have used her colleague's death and everyone's grief for her own personal gain? If so would she pretend to be pregnant by Seeley or try to pass off someone else's baby as his?

He needed answers and needed them now. All this thinking of Booth and that woman was making him sick to his stomach. That's when the feeling he was going to puke made its self known. He quickly jumped up from his seat and ran up the steps to the first floor's bathroom. He had just made it before he lost the contents of his stomach. After he was done he felt a cool wash rag on his face and a cup of water was handed to him.

He quickly rinsed his mouth out and flushed the toilet.

"Thanks," Tony said past his sore throat.

"No problem. Are you alright now or do you still feel sick?"

"I'm fine; I was just thinking and worrying myself sick. I'll be fine."

"If you're sure that's the reason." Gibbs was skeptical as to if that was really the case or not. But thinking about it what other reason would there be for Tony to get sick like that?

"Yea I'm sure. So I guess I'm going to go talk to Seeley and get this all straightened out and maybe give him the benefit of the doubt. I just want all of the wondering and worrying out of the way." Tony didn't mention his thoughts on the kid's biological father he really didn't need to jinx himself now.

Gibbs realized then that he needed to be supportive and he hoped for the best for Tony and his kids. If the best for them was being with Seeley then he wished nothing but. Like the saying went 'if you love someone, set them free. If they come back they're yours; if they don't they never were'. That's what he needed to do, let Tony go and see about Seeley but if he doesn't find what he wants he may come back. He couldn't hold Tony back from true love or happiness. So even though they were never together maybe it could still work the same way.

"I think that's a good idea. You need to be one hundred percent behind your choice or you'll always have that question in the back of your mind if you did the right thing or not. So when do you think you're going over there?"

"I might go over later today. I'm not sure if I want to take the kids with me or not. I mean if we get into a fight I don't want them to have to see that. But I know if I had the kids taken from me the only thing I would want to do is see my kids. I mean they can always just play in their rooms while Seeley and I talk. Great now I'm rambling on and on. Sorry," Tony said while looking up at Gibbs with a sheepish smile on his face.

"It's alright, I get it you always ramble when you're nervous but it gets worse when you're unsure of something."

"Do not!" Tony said trying to look angry but failed when the corner of his mouth rose and he gave a small chuckle.

Gibbs couldn't help but laugh along. "Okay if you think you don't." Growing serious Gibbs looked over at Tony. "It's all up to you on whether or not you take the boys with you or not. I'll watch them if you need me to."

"Thanks Gibbs. You've been really helpful and I can't thank you enough. You're great with the kids and took us in when most people would have turned us away."

Gibbs could feel his face heating up, "It's no problem at all. You're kids are amazing and I don't mind at all spending time with them or you. If things go well with Booth, they can still come over when ever they want."

"Thanks Gibbs, that means a lot to me."

Gibbs only nodded. "Alright how about some lunch."

***JLC***

Hearing the door open and shut, Gibbs smiled as he heard the sounds of six little feet running. "Boys, what did I tell you about running!" "Sorry."

Gibbs was still laughing as Tony walked down the steps. "It is not funny Gibbs! They could get hurt, but of course they got their stubbornness from their father." Tony said while trying to keep a straight face.

"Yea they got it from only one of their fathers." Gibbs good-naturedly said sarcastically

"Ha ha ha you're so funny Gibbs. So I'm going to go and talk to Seeley. I've decided to take the kids with me. Earlier they were asking about him and plus I feel bad for keeping them away from him, I know how I would feel if he did the same. So I may not be back if all goes well. But I'll call you either way, if that's alright with you?"

"Yea that's no problem. And good, they should see their father no matter what. Any father would be crazy if he didn't want to see his kids, and I saw how he was with them he's probably out of his mind without seeing them."

"Yea I know. He's always been good with them and he really loves them. I just hope that if anything does happen they're not caught in the middle of it."

***JLC***

"Hold on, I'll be right there," the voice was muffled behind the closed door, hearing that voice sent butterflies all through out his stomach, as Tony waited for the door to be opened. Who knew he would be knocking at his own door to be let in? it just didn't feel right to be opening the door to the house now even though it was still his house.

"Hey," was the only thing Tony could get out as he came face to face with the one person he couldn't live without, the one who had caused this while problem.

"Tony, I'm so glad you're here." Booth couldn't believe his eyes. He hadn't thought Tony would show up at the house and especially not with the kids. He looked down into the sleepy faces of his twins and back up into the green eyes of his youngest in the arms of his husband. He wanted nothing more for this whole thing to be over and fall asleep with his husband in his arms but he knows they have to talk through this.

"Come on in. I'll take the twins to their room they look exhausted."

"Yea they haven't slept since their nap," Tony commented as he watched Seeley grab the twins who had outstretched their arms up to him. "I'll take Trav up to his."

Once the kids were put down for bed Tony walked down the steps into the living room. Seeley had made up two mugs of coffee; one black and the other full of hazelnut creamer and sugar. He set them on the coffee table so they could sit and talk.

Tony sat on his favorite side of the couch and put a blanket around him. The smell of the blanket permeated to his nose bringing the relaxing smell of home to his nose. It brought him back to a simpler time when everything was easy. They both tried to find a way to start the conversation nut neither could come up with anything to say.

Finally, Booth found his voice, "Tony I know I messed up and I cant change that but I miss you so much. We haven't been apart for long except for work and I could barely stand that. I need you in my life and in our home with our kids. You are the other part of me. So please baby, come home."

"I…"

**TBC**

**A/N: I know awful place to stop but more will be coming soon. I hope you're enjoying the story so far. Thanks for all the comments about which pairing. I'm still not totally sure which pairing I'm going with as of now because I have two different endings I'm thinking of. So I'm going to need some more votes as to which pairing Booth/Tony or Gibbs/Tony.**


	7. Chapter 7

**Secret Life of a Special Agent**

_Tony sat on his favorite side of the couch and put a blanket around him. The smell of the blanket permeated to his nose bringing the relaxing smell of home to his nose. It brought him back to a simpler time when everything was easy. They both tried to find a way to start the conversation nut neither could come up with anything to say._

_Finally, Booth found his voice, "Tony I know I messed up and I cant change that but I miss you so much. We haven't been apart for long except for work and I could barely stand that. I need you in my life and in our home with our kids. You are the other part of me. So please baby, come home."_

"_I…"_

"I…"

Tony was so unsure of himself and his decision. Could he really come home to Seeley with knowing he cheated on him? He knew that the love was still there between the two of them it and he still trusted him but how far could both of those things go? Was he willing to take back a man who cheated on him with some woman? Then the thought of the baby went into his head, sending off more thoughts he would rather have ignored. Looking at Seeley now though Tony wanted nothing more than to cuddle into bed with his head on Seeley's chest and fall into a restful sleep. Maybe they could make it work and be happy again.

"I still love you, but I don't know how this will work if I do come back. What about that woman Temperance and the baby? I can't go through all of that and I am not putting the kids through that. They shouldn't have to deal with all of this just because something like this happened."

"I know they shouldn't have to and neither should you. It's unfair to you, and I don't want you to have to go through this. I'm going to ask Temperance to do something just so I'll know for sure; I'm going to ask her to have a paternity test done on her child, just so I'll know for sure. I don't even know why all of this happened; to be honest I don't remember anything from that night especially not being with her."

Tony only nodded his head. He prayed to any deity that would listen to let that test be negative and that this was all some sort of big misunderstanding. Maybe he was never with her or maybe the child wasn't Seeley's. Just then Exhaustion caught up with Tony, a loud yawn escaped his mouth.

Seeley gave a small chuckle at hearing his husband yawn. Once Tony began to get tired there was no way to get him back to the land of the awake. So he did the only thing he could think of.

"Come on Tone, you're tired why don't you go upstairs and sleep. I'll feel better knowing you're not practically asleep behind the wheel. The kids are already asleep in their beds."

Another yawn escaped as he nodded. But he was too tired to even stand. As if sensing this Booth walked over and picked Tony up. Even though Tony was not the smallest man, Booth was always able to pick him up as he was bigger than Tony and a little older.

Booth couldn't help the small smile that graced his face as he held Tony close and felt Tony snuggle farther into his chest.

Pulling back the covers, Seeley laid Tony down on his side of the bed and covered him. He had removed his shoes and placed them in their usual spot in the corner. Seeing Tony snuggled onto his side, Booth was brought back to when both of them were younger and in so much love.

They were the couple no-one was surprised to see together. They were so alike it was crazy to many that they got along so well. Even when he was young and had his whole future ahead of him he still knew him and Tony were going to be together, get married, have kids, and grow old together. If only that were still true, he could only hope and pray that they stayed together after the stunt he pulled and the huge mistake he made.

Booth made his way to check on the kids. He was all too happy to have the kids back under the same roof. He had missed them so much. Seeing the sleeping face of his twins brings a smile to his face. The thought that the two most mischievous kids could look peaceful and innocent in their lives was too funny for Booth. Gently placing a kiss to their forehead Booth sent a silent prayer up to anyone who would listen for his mistake to not lead to the demise of his once happy family.

Closing the door slowly, Seeley made his way to Travis' room. Travis was still at that age or stage where he didn't sleep all the way through the night; he would wake up early and just lay there unless he wanted something. Travis was what you would call a good baby, he took naps with no problems, and he would play in his play pen for hours and hardly cried. Travis was also their miracle baby. After the twins were born, the doctor had told them that Tony may not be able to carry any more children or they could both be in danger. When they discovered he was pregnant again they made the tough decision to go through with it and they got a third beautiful son out of it.

Looking in on Travis, Seeley saw he was still peacefully asleep and not wanting to bother him he slowly backed out of the room and closed the door silently.

He made his way back to his room, standing in the door way observing a sleeping Tony. He was starting to question himself. Should he go lie down and sleep? Did he have any right to sleep next to Tony after what he did?

"Are you coming to bed or not?" A whispered sleep-fogged voice asked in the dark.

Seeley walked over to the once sleeping Tony and bent down to be face to face. "I didn't know if I should or if you would want me to."

Tony gave a slight nod, "I want you in here with me. We'll figure everything out later but right now I'm tired and cold, and my husband should be warming me up."

Seeley chuckled lightly at Tony's usual remark. Shedding all of his close but his boxers, he shimmied under the blankets to lie on his back looking up at the ceiling. Not long after he felt the bed move and felt a hesitant hand make its way to his chest. Waiting and holding his breath Seeley couldn't help but smile when he felt Tony's head gently fall on his chest, a light breathe tickle his chest. Tony snuggled in further to the heat Seeley's body was giving off leading his arm to wrap around Tony. Seeley leaned down and kissed the soft hair on Tony's head like he had done a million times, but this time it was different; it felt like so much more. It was a promise to be faithful, a promise to always be there and a promise to never mess up again.

"Mmm g'night." A sleepy Tony breathed out.

"Goodnight Babe."

And with that they both fell asleep with the hope of tomorrow, of the future; their future together.

**TBC:**

**Sorry about the huge delay and the short chapter. I'm going to try wrapping this up soon. I'm studying for finals, studying for classes, work and a bunch of other things. I am not giving up on this story. **


	8. Chapter 8

**Secret Life of a Special Agent**

****§****

_Tony gave a slight nod, "I want you in here with me. We'll figure everything out later but right now I'm tired and cold, and my husband should be warming me up."_

_He shimmied under the blankets to lie on his back looking up at the ceiling. Not long after he felt the bed move and felt a hesitant hand make its way to his chest. Waiting and holding his breath Seeley couldn't help but smile when he felt Tony's head gently fall on his chest, a light breathe tickle his chest. Tony snuggled in further to the heat Seeley's body was giving off leading his arm to wrap around Tony. Seeley leaned down and kissed the soft hair on Tony's head like he had done a million times, but this time it was different; it felt like so much more. It was a promise to be faithful, a promise to always be there and a promise to never mess up again. _

"_Mmm g'night." A sleepy Tony breathed out._

"_Goodnight Babe."_

_And with that they both fell asleep with the hope of tomorrow, of the future; their future together. Seeley chuckled lightly at Tony's usual remark._

****§****

3 months later

"Boys you better be ready, we have to leave soon!" Tony yelled up the stairs as he was putting his sons' toys away.

When he was done he looked around to be sure everything was done he jumped at the feeling of two strong arms around his waist and smiled when he felt lips on his neck. He backed into the strong body, reveling in the heat of the familiar body. Leaning his head back he smiled looking up into the eyes he loved, and laughed as he was being kissed gently but passionately.

"Ewwy," came a joking voice and three little giggles.

The two men reluctantly pulled apart to look at the three smiling faces. Tony felt a deep chuckle going through the man hugging him close and couldn't help but laugh along.

"Oh you boys think that's funny? Well you know what else is funny? The tickle monster getting you!" With that Tony took after the boys who let out high pitched squeals and ran away laughing.

When all was done Tony was lying down on the living room floor with his three boys who were all tired.

"You guys look comfy." A voice said from the doorway.

"DADDY!" All three little boys yelled as they jumped up and almost tackled Seeley who just laughed.

Seeley had two boys in his arms and one hanging on his leg as he made his way over to Tony who had still yet to get up from lying down. Seeley smiled his heart-warming smile that only Tony ever saw.

"You better get up too, we're going to be late."

"Yea, yea, yea I'm up."

Tony walked over to Seeley and hugged him while the boys grabbed their bags. They all piled into the SUV to go for a ride.

As they pulled up to the two storied house the boys were practically bouncing up and down with excitement. The vehicle had just been put into park as the boys opened the door and ran over to the front door right as it was opening. A smiling woman opened the door and held her arms open, which the boys took full advantage of as they launched themselves at her.

"Hey be careful boys. You don't need to bulldoze everyone down." Tony yelled as he shut the door and was grabbed around the waist by Seeley.

"Oh they're no problem at all. I miss having kids around playing." The woman laughed.

"Alright come on boys, into the house and put your bags in your rooms."

"Okay Uncle Jefwo." Travis answered as he followed behind his older brothers to the upstairs bedrooms.

"Hey Tony, Seeley." Gibbs said as he saw them and put his arm around the woman.

"Hi boss and of course hello to the beautiful Alice, how are you?"

"Oh still such the charmer. I'm very well, how are you?" Alice answered laughing at Tony's usual remarks.

"I'm very well also. Thank you two so much for taking them for the weekend. We really need to get away after the whole Temperance fiasco."

"Hey don't worry about it, we don't mind at all and we love spending time with the kids. So you two better get going before you miss your plane. Have fun in Italy." Gibbs spoke up. He had become more talkative since meeting Alice, who he met shortly after he got over the unrequited love of Tony. Gibbs discovered that he was happy when ever Alice was around and he had started smiling more. They had started dating for a month until they both realized that they didn't want to wait for the next step when they loved each other so much. They had waited around for the special someone for years and they weren't about to pass up on that love that they had lived so long without. They had moved in together and haven't looked back since.

"Thanks you two. So you have our numbers and the hotel number where we're staying. And you know what the boys like and don't-"

"Tony we know all of this stuff so don't worry we have everything under control." Gibbs said with a slight smile at his agent's protectiveness and worry over his sons.

"I know you do its not that it's just, we haven't been gone this long away from them and I'm nervous." Tony said while looking down but gave a slight smile when Seeley gave his hand a squeeze and moved in closer to him.

"Alright well you two better get going. Boys get down here before your parents leave!" Gibbs yelled up the steps and not long after they all heard little feet puttering down the steps.

After long hugs, big kisses and plenty of 'I love you's Tony and Seeley drove to the air port.

***JLC***

Entering the hotel by the water Tony couldn't help but look around in wonder at being back in Italy one of the many places he counted as home. After traveling to Italy almost every summer as a child and during college Tony had grown fondly attached to the place.

The trip marked their fresh start and the new beginning they were taking together. They were planning on renewing their vows and do it in front of their friends and family, unlike when they were younger.

After much investigating, it was discovered that Temperance had lied not only to Booth but also her ex-boyfriend. The baby was not Booth's but an old boyfriend who she had a fling with. Her obsession for Booth became too much for her to handle and wanted a way to make sure he would be with her. A bug thing she had not anticipated on was Booth having a husband and a family. Tony did not rest until he found out the truth of the whole accusation of Booth being the father. When confronted over the fact of paternity something snapped and she charged after Tony and was arrested and was tested for her level of sanity. The results were that it was in her best interest to go to a facility for further help.

Tony and Seeley were both glad that she was out of their life and they didn't have to worry anymore about the lies or the woman and her baby. They could just forgive and forget and get back to their lives and kids.

Seeley walked behind Tony and took him in his arms. They stood by the large window and watched the sun go down over the water and watched the boats dock and sway in the water. Nothing could top that romantic and relaxing moment for them.

Tony shivered as he felt the first kiss to his neck and moved it to the side to be more accommodating. It soon escalated as hands were moving all over his body and little nips were sending sparks down his spine straight to his groin. Turing around Tony seized Seeley's mouth in a passionate and searing kiss. Seeley pulled him until they were almost crushed together. Tony stepped back until they were against a wall and hooked his leg behind Seeley's back, grinding their hips together. Booth growled low in his throat at the onslaught of everything Tony and what he was doing. He picked Tony up and Tony wrapped his legs around Seeley's hips as Seeley began to walk. Tony couldn't help but laugh as he was thrown onto the bed but stopped as Seeley made his way on top of him.

After multiple rounds of getting reacquainted, Seeley and Tony lay cuddled together on their bed. Seeley couldn't think of a better moment then this. Looking down at the man who was using his chest as a pillow Seeley couldn't help but feel an immense love for the man who was his soul mate, best friend and father of his children. Hearing and feeling the constant rise and fall of his lover's chest soothed him to a restful sleep with hopes for the future running through his head. He knew they would overcome everything and come out closer than ever before.

**The End**


End file.
